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   &#160;<span id="projectnumber">0.4.0</span>
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      <li class="navelem"><a class="el" href="namespacemoltk.html">moltk</a>      </li>
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<div class="title">moltk::Aligner Member List</div>  </div>
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This is the complete list of members for <a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a>, including all inherited members.<table>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align</a>(const Alignment &amp;, const Alignment &amp;)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a99008604e446e2adc4f0df7e4afd6c9e">Aligner</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#ae88d9a29786521dacbf511a8097bb063">allocate_dp_table</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a401c10c0e6923397ba8227ef31137aca">b_local_aligner</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a729b4f44dd7e0411b0acdde5c1561af5">clear_positions</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#ace84085990dcff6eac7f8baf8a5c5d9a">clear_scorer</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a38863ca0eb76e0241abedefaa69b0048">compute_cell_recurrence</a>(int i, int j)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a5c0dfb557f1fe73f8b0b6dc6eb029ab2">compute_cell_recurrence_freeE</a>(int i, int j)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a8d28c9bb018c6d4913e305c36093eeb0">compute_cell_recurrence_freeEF</a>(int i, int j)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#ac1c097af307968d9caf76242977a288d">compute_cell_recurrence_freeF</a>(int i, int j)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a66756b5e61b63ee8f26b6abb7b1de02e">compute_recurrence</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#ac6170833b8d8c742719e45186aff85b8">compute_traceback</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a11e4f5632b62483c32b1169754f2261d">dp_table</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a> typedef</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">DpTable</a> typedef</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a7d364467fa46629a81c3adbcc2cd2692">get_default_scorer</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [static]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#aeb69db8c0ba583694b389d37e2f9f05b">get_end_gaps_free</a>() const </td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a2a94cf962985576ec14640ee519fa371">get_shared_aligner</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [static]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> typedef</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a5a7bc14266d9a09c00133aeee98ae039">init</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a47aa0cc272a3aa95d23dfec38d7883b0">initialize_dp_row</a>(size_t rowIndex, DpRow &amp;row)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a00167b2c4ea9d0e01e5ed56e8946b713">initialize_dp_table</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#afedcb89907a4037bccb3754a6e2eb2a3">m</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a3ee7cf4bee96c010e3644615f45f7dcc">n</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#afc1bffe01773a0be7eba8a0961f75122">output_alignment</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#ac708decb0f2bc0a6c5563ee975f8e5a4">query_alignment</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">scorer</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a95bf66d275c37f120f9698a441eaa18b">seq1</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a934541c902699844d3fbcc4b04e96444">seq2</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a1a3475cfc191d9c7efa26f26ba4436b8">set_end_gaps_free</a>(bool f)</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208">Stage</a> enum name</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abbf7d1ed6268e8d3a7b8725a59b69d9f">STAGE_ALLOCATED</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a2877fdfe8fa9345c485dc69d2f5200ca">STAGE_EMPTY</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a22d74955c68c209611ee163f65aa2cc7">STAGE_RECURRENCE_COMPUTED</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a42a9835d9845ffd8795ddcf578b20696">STAGE_SCORER</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a5ab4a5ba046f6d4b741e687baecbff92">STAGE_SEQUENCE</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208ad21d8375c870feed36071a180c7a797c">STAGE_TABLE_INITIALIZED</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208ae27f4f916fb73fc17d2310072d718cb0">STAGE_TRACED</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#aa900f963fef40a9b258c93c32d7c2db1">target_alignment</a></td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55baed40c1c6e565bbbee48d601aaafe0812">TRACEBACK_DONE</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bab5353821ddae5b7ea5c6ce44d2d62d81">TRACEBACK_LEFT</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba4de2c99df6a5314ce86b8d850734d220">TRACEBACK_NOT_INITIALIZED</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba6da2cb4f6502904671847ec848503045">TRACEBACK_UP</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bae1838f55d1bd7835d79ffee07b42467e">TRACEBACK_UPLEFT</a> enum value</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b">TracebackPointer</a> enum name</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Aligner.html#a9855904b20ecd75a1e44cfa955dd4f97">~Aligner</a>()</td><td><a class="el" href="classmoltk_1_1Aligner.html">moltk::Aligner</a></td><td><code> [virtual]</code></td></tr>
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